Farmers, transport companies and ship operators involved in the export of live animals face tougher controls over their business as ministers seek to allay welfare concerns over the treatment of livestock.

Government inspectors are already said by ministers to be checking all shipments through Ramsgate in Kent, the only port now involved in the trade – albeit reluctantly – and this will continue until the government is satisfied "there is no longer a high risk" to animals.

Lorry companies and shippers will also not be allowed to give short notice of shipments to the agency, the Department for Environment, Food and Rural Affairs (Defra) said on Wednesday. This happened last month in an attempt to evade protests by welfare campaigners at the port where more than 40 sheep had to be destroyed on the advice of the RSPCA after an incident in September.

Lame and injured sheep had been found unfit to travel after being transported on a lorry from Northamptonshire. Two others drowned. The deaths happened after the RSPCA gave a report to the council highlighting the port's inadequate facilities.

There has also been growing unease among MPs over live exports following another incident, in November, when the ferry Joline was forced by bad weather to turn back while en route to Calais with hundreds of sheep.

The new measures are designed to ensure a government vet is always within an hour's travel of the port. Lorry companies carrying animals for export face more controls over their journey logs to ensure animals are not held in conditions that break EU welfare rules and exporters will also have to prove they have suitable contingency plans for emergencies.

The food and farming minister David Heath said: "We would prefer to see animals slaughtered as close as possible to where they are reared, but while live animal exports remain a legal trade under European laws we must allow it to continue.

"Our animal welfare laws must be followed to the letter so that no animal is made to suffer during transport. Until I am entirely satisfied that there is no longer a risk to the welfare of animals at Ramsgate, I have ordered AHVLA [the Animal Health and Veterinary Laboratories Agency] to check every consignment of live animals scheduled to pass through Ramsgate. I want a zero tolerance approach – if we find any evidence of slipping welfare standards then we will not hesitate to take action."

Heath added that "following the shocking events at Ramsgate on 12 September, we are tightening up our procedures to deal with breaches of welfare standards. It is completely unacceptable that more than 40 sheep died unnecessarily and I am determined that this cannot happen again."

Thanet district council, which owns Ramsgate port, had been trying to suspend the trade because of what it sees as insufficient facilities at the port but it decided not to contest a judicial review of that policy by companies involved in the exports. It said it could not risk spending public money on a case its lawyers said it would probably lose.

The council's decision also reflected its understanding that a review undertaken by Defra was unlikely to require additional facilities to be provided at or by the port. Heath's announcement made no reference to any.

The RSPCA intends to take up the legal fight to ban further live animal exports from Ramsgate. It has launched a fighting fund to pay for it. Its chief executive, Gavin Grant, said: "We will not step away from this – the battle to end live exports is far from over. The lack of proper facilities at the port of Ramsgate and the failure to thoroughly inspect animals as they loaded aboard ship are both unacceptable. This cannot go on.

"We are here for the animals and they deserve their case to be heard in court. To do that we need the public's help. We have a highly professional and successful legal team but going to court is not cheap.

"The RSPCA relies entirely on the public to fund our work and I am certain that they will dig deep and ensure the animals get their day in court."

Last month, the company running the Joline from Ramsgate to Calais claimed the council had been tipping off protesters so they could mass at the port when sailings were planned, an accusation denied by the authority and protesters.